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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, database, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-02-15 09:22:07 | 210 | ||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software toolkit, software resource | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-02-15 09:17:54 | 31 | ||||||||
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GenVision Resource Report Resource Website 1+ mentions |
GenVision (RRID:SCR_001166) | GenVision | commercial organization, software resource | A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig. | genome, image, visualization, graphic, map, gene expression, contig, genetics |
is listed by: OMICtools works with: Lasergene's SeqMan Pro |
Commercial | OMICS_02135 | SCR_001166 | GenVision - Software for Publication-Quality Illustrations, DNASTAR GenVision | 2026-02-15 09:18:03 | 1 | |||||||
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University of Delaware Skate Genome Project Resource Report Resource Website 1+ mentions |
University of Delaware Skate Genome Project (RRID:SCR_005300) | Skate Genome Project | access service resource, core facility, service resource | Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea. | skate, genome, genomics, bioinformatics, sequencing, annotate, sequence, workshop |
has parent organization: North East Cyberinfrastructure Consortium has parent organization: University of Delaware; Delaware; USA is parent organization of: SkateBase |
Available to external user | nlx_144349 | SCR_005300 | , University of Delaware, Genome Project, Skate | 2026-02-15 09:19:03 | 1 | |||||||
|
Genomedata Resource Report Resource Website |
Genomedata (RRID:SCR_004544) | Genomedata | source code, software resource | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-02-15 09:18:45 | 0 | ||||||
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Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research. | nucleic, acid, microarray, assay, database, development, analysis, genome, assembly, pathway, data, gene, expression, metagenomics |
is listed by: Eagle I has parent organization: Montana State University |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156405 | http://cores.montana.edu/bioinformatics/ | SCR_009937 | , Montana State University, core facility, MSU, Bioinformatics Core Laboratory | 2026-02-15 09:20:11 | 0 | |||||||
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FaST LMM Resource Report Resource Website 1+ mentions |
FaST LMM (RRID:SCR_015506) | software toolkit, software resource | FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets. | gwas, association study, heritability, single-snp, snp-set, genome | Free, Available for download | SCR_015506 | Factored Spectrally Transformed Linear Mixed Models, fastlmm | 2026-02-15 09:21:20 | 6 | ||||||||||
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iPiG Resource Report Resource Website |
iPiG (RRID:SCR_016164) | iPiG | software application, standalone software, software resource | Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. | integration, peptide, spectrum, match, genome, browser, visualization, experiment, pms, ms, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian |
Robert Koch-Institute | PMID:23226516 DOI:10.1371/journal.pone.0050246 |
Free, Available for download | biotools:ipig, OMICS_06913 | https://bio.tools/ipig https://sources.debian.org/src/ipig/ |
SCR_016164 | iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations | 2026-02-15 09:21:02 | 0 | ||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-02-15 09:22:09 | 5 | |||||
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ProtHint Resource Report Resource Website 10+ mentions |
ProtHint (RRID:SCR_021167) | software toolkit, software resource | Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences. | Predicting and scoring hints, form of introns, start and stop codons, genome, mapping, spliced aligning, predicted genes, database, reference protein sequences | has parent organization: Georgia Institute of Technology; Georgia; USA | Free, Available for download, Freely available | SCR_021167 | 2026-02-15 09:22:32 | 45 | ||||||||||
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Plant Metabolic Network Resource Report Resource Website 100+ mentions |
Plant Metabolic Network (RRID:SCR_002888) | project portal, data or information resource, portal | Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. | e. coli, gene, arabidopsis, barley, coffee, database, genome, grass, homolog, maize, medicago, oats, pathway, pepper, plant, potato, rice, rye, sorghum, species, taxonomy, tomato, wheat, ontology | lists: PlantCyc | nif-0000-25602, SCR_003778, nlx_15806 | SCR_002888 | Plant Biochemical Pathway Databases | 2026-02-15 09:18:25 | 149 | |||||||||
|
DOE Joint Genome Institute Resource Report Resource Website 500+ mentions |
DOE Joint Genome Institute (RRID:SCR_003045) | DOE JGI, JGI, | organization portal, data or information resource, portal | Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. | genomics, sequencing, computational analysis, clean energy, environment, biotechnology, nucleotide sequence, protein, genome, bacteria, microorganism, fungal colony, fungal community, dna, phenotype, molecular biology, life science, genomics, genetics, nature, nurture, ecology, bioenergetics, high-throughput sequencing |
is listed by: re3data.org has parent organization: University of California; California; USA is parent organization of: Microbial Genetics Resource at JGI is parent organization of: JGI Genome Portal is parent organization of: Genomes Online Database is parent organization of: IMG System is parent organization of: Classifier for Metagenomic Sequences is parent organization of: MycoCosm is parent organization of: Plant Genome Resource at JGI is parent organization of: Classifier for Metagenomic Sequences is parent organization of: Phytozome is parent organization of: IMG is parent organization of: Metagenomics Program at JGI is parent organization of: Assembly Likelihood Estimator is parent organization of: 1000 Fungal Genome Project is parent organization of: Bestus Bioinformaticus Tools is parent organization of: Bestus Bioinformaticus Duk is parent organization of: Bestus Bioinformaticus Merge is parent organization of: Reformat |
DOE | Free, Freely available | nif-0000-30425 | SCR_003045 | DOE Joint Genome Institute - Enabling Advances in Bioenergy & Environmental Research, Department of Energy Joint Genome Institute, Joint Genome Institute | 2026-02-15 09:18:28 | 689 | ||||||
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Human Gene Connectome Resource Report Resource Website 1+ mentions |
Human Gene Connectome (RRID:SCR_002628) | HGC | data or information resource, data set, software resource | Data set containing a gene-specific connectome file for each human gene and computer programs for ranking lists of genes within a gene-specific connectome, clustering and plotting the genes by the functional genomic alignment (FGA) approach, and generating gene-specific connectomes. The programs were developed and tested on Mac and Linux systems. The external software required for running these programs is open-source and free of charge. The HGC is the set of all biologically plausible routes, distances, and degrees of separation between all pairs of human genes. A gene-specific connectome contains the set of all available human genes sorted on the basis of their predicted biological proximity to the specific gene of interest. The HGC is a powerful approach for human genotype-phenotype high-throughput studies, for which it can be used to rank any list of genes within a gene-specific connectome for an experimentally validated core gene. Functional genomic alignment (FGA) is equivalent to traditional multiple sequence alignment (MSA), except that it clusters genes in trees on the basis of the functional biological distance between them predicted by HGC, rather than on the basis of molecular evolutionary genetic distance. This method is therefore more suitable for disease and phenotypic studies. | gene, disease, phenotype, genome, connectome, functional genomic alignment |
has parent organization: Rockefeller University; New York; USA is parent organization of: Human Gene Connectome Server |
NCATS 8 UL1 TR000043 | PMID:23509278 | Free | nlx_156050 | SCR_002628 | 2026-02-15 09:18:21 | 5 | ||||||
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National Genome Research Network Resource Report Resource Website 10+ mentions |
National Genome Research Network (RRID:SCR_006626) | NGFN | organization portal, data or information resource, portal | The program of medical genome research is a large-scale biomedical research project which extends the national genome research net (NGFN) and will be funded by the federal ministry of education and research (BMBF) from 2008-2013. Currently the program includes two fields: * Research ** NGFN-Plus: With the aim on combating diseases that are central to health policy, several hundred researchers are systematically investigating the complex molecular interactions of the human body. They are organized in 26 Integrated Genome Research Networks. * Application ** NGFN-Transfer: The rapid transfer of results from medical genome research into medical and industrial application is the aim of the scientists from research institutes and biomedical enterprises that cooperate in eight Innovation Alliances. AREAS OF DISEASE * Cardiovascular disease * Cancer * Neuronal diseases * Infections and Inflammations * Environmental factors | genome, research, gene, disease | Cardiovascular disease, Cancer, Neuronal disease, Infectious disease, Inflammation, Disease linked to environment | BMBF | nlx_151595 | SCR_006626 | NGFN - National Genome Research Network, German National Genome Research Network | 2026-02-15 09:19:19 | 26 | |||||||
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WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation Resource Report Resource Website 10+ mentions |
WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) | WebApollo | service resource, source code, software resource, production service resource | WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer | sequence, annotation, genome |
has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Georgetown University; Washington D.C.; USA |
nlx_144381 | SCR_005321 | WebApollo - A Web-Based Sequence Annotation Editor for Community Annotation | 2026-02-15 09:18:56 | 13 | ||||||||
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NextPolish Resource Report Resource Website 50+ mentions |
NextPolish (RRID:SCR_025232) | software application, source code, data processing software, software resource, data analysis software | Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome. | fix base errors, SNV/Indel, genome, noisy reads, correct error bases, reference genome, | Free, Available for download, Freely available | SCR_025232 | 2026-02-15 09:22:56 | 73 | |||||||||||
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HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-02-15 09:24:05 | 1 | ||||||||||
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NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects Resource Report Resource Website |
NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) | NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects | project portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV | genome, sequencing |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_003205 | 2026-02-15 09:18:28 | 0 | |||||||||
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Gramene Resource Report Resource Website 500+ mentions |
Gramene (RRID:SCR_002829) | GR | data or information resource, database | Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. | crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Gene Ontology is related to: Plant Ontology is related to: Trait Ontology is related to: EnvO is related to: BioCyc has parent organization: Cold Spring Harbor Laboratory has parent organization: Cornell University; New York; USA is parent organization of: Trait Ontology is parent organization of: Plant Environmental Conditions is parent organization of: Plant Trait Ontology is parent organization of: Cereal Plant Development Ontology is parent organization of: Cereal Plant Gross Anatomy Ontology |
USDA IFAFS 00-52100-9622; USDA 58-1907-0-041; USDA 1907-21000-030; NSF 0321685; NSF 0703908; NSF 0851652 |
PMID:21076153 PMID:17984077 PMID:16381966 |
Free, Freely available | r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene | https://bio.tools/gramene https://doi.org/10.17616/R3GG7M |
SCR_002829 | GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL | 2026-02-14 02:00:19 | 778 | ||||
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HemBase Resource Report Resource Website 1+ mentions |
HemBase (RRID:SCR_002880) | data or information resource, database, resource | Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | erythroid, erythroid cell, erythroblast, expressed sequenced tag, transcriptome, gene, erythropoiesis, cytogenetic location, hematology, genome, red blood cell, progenitor cell, precursor cell, chromosome |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Anemia, Erythroleukemia, Malaria, Erythroid cell related disease | NIDDK 1ZIADK025098 | PMID:14681483 PMID:10409428 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02949 | SCR_002880 | Hembase | 2026-02-14 02:00:27 | 4 |
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